Neuro Advances

Bio-Image Informatics: Better Tools
for Neurology and Neurological Research


Imaging advances have provided invaluable insights into the functioning of the human body. Now, powerful tools are being developed to better use this information for diagnosing and treating illness and injury. 


Clinicians and researchers who study the brain rely on several advanced technologies: magnetic resonance imaging to pinpoint brain tumors and guide neurosurgeons; positron emission tomography to locate amyloid plaques in the brains of Alzheimer’s patients; and advanced microscopy techniques to better view biological processes at the cellular and molecular levels. These cutting-edge imaging technologies generate enormous quantities of data that present a considerable challenge to analyze, store and access.


“Digital imaging is pervasive in research and medical applications today, yet much of the analysis is done laboriously by humans,” says B.S. Manjunath, PhD, professor of electrical and computer engineering at the University of California, Santa Barbara (UCSB), and director of the university’s Center for Bio-Image Informatics, an interdisciplinary research effort encompassing biology, computer science, statistics, multimedia and engineering.


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UCSB and Cottage are in the preliminary stages of developing a joint research program with planned facilities on the campus for translational medical research.

— Prof. Francis J. Doyle III
Associate Dean for Research
College of Engineering, UCSB


“The infrastructure to manage this information is lagging behind the imaging technology itself,” Dr. Manjunath adds. “Much critical-analysis information is not available to the decision makers. Doctors, for example, currently cannot easily search through image records to make comparisons, retrieve pertinent information and arrive at informed decisions.”


To maximize the use of these imaging technologies, the UCSB team is developing a system to help manage microscopy images and quantitatively analyze bio-image data. The aim is to advance understanding of biological processes by developing and utilizing advanced techniques incorporating imaging, pattern recognition and data mining.


The Bio-Image Semantic Query User Environment (Bisque) system integrates image analysis with database management functionalities, creating a powerful tool for the exchange and exploration of biological images. Bisque handles up to 5-D images, and allows users to store, access, analyze, annotate and share images and related data with colleagues. Now being used at several laboratories in the united states and overseas, the system’s nascent online repository includes more than 13,000 biological images.


Managing Metadata

To bridge the gap between microscope and database, researchers with the center for Bio-Image Informatics have developed another application—scientist’s digital notebook—to help users create the metadata required by the Bisque database and rapidly upload images to the system. Now one of the most popular downloads from the center’s website, the application allows researchers to manage large collections of biological images and related metadata on local machines and within the Bisque system.


The aim is for tools like these to enable researchers—and future clinicians—to take full advantage of cutting-edge imaging technologies to help patients.


To download the Bisque Database or Digital Notebook applications or learn more about the UCSB Bio-Image Semantic Query User Environment system, visit


by Anna Davison, Senior Writer


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